<tool id="extract_wrapper" name="Extract" version="0.2">
  <description></description>
  <requirements>
    <requirement type="package" version="3.02">glimmer</requirement>
  </requirements>
  <command interpreter="python">
    extract_wrapper.py --exSequence $exSequence --exCoords $exCoords
    #if $ex2Fields
    --ex2Fields
    #end if
    #if $exDir
    --exDir
    #end if
    #if str($exMinLen)
      --exMinLen=$exMinLen
    #end if
    #if $exNoStart
    --exNoStart
    #end if
    #if $exNoStop
    --exNoStop
    #end if
    #if $exNoWrap
    --exNoWrap
    #end if
    --exOutput $exOutput --logfile $logfile
  </command>

  <inputs>
    <param name="exSequence" type="data" format="fasta" label="DNA sequence to be analyzed" help="FASTA format" />

    <param name="exCoords" type="data" format="glimmer_coords" label="Coordinates produced by Long-ORFs" />

    <param name="ex2Fields" type="boolean" checked="false" label="Output sequence in 2 fields (-2, --2_fields)" help="Output each sequence as 2 fields (tag and sequence) on a single line." />

    <param name="exDir" type="boolean" checked="false" label="Specify sequence direction (-d, --dir)" help="Use the 4th column of each input line to specify the direction of the sequence. Positive is forward, negative is reverse. The input sequence is assumed to be circular." />

    <param name="exMinLen" type="integer" value="" optional="true" label="Minimum length of sequence (-l, --minlen)" help="Don't output any sequence shorter than n characters." />

    <param name="exNoStart" type="boolean" checked="false" label="Omit first characters (-s, --nostart)" help="Omit the first 3 characters of each output string." />

    <param name="exNoStop" type="boolean" checked="false" label="Omit last characters (-t, --nostop)" help="Omit the last 3 characters of each output string." />

    <param name="exNoWrap" type="boolean" checked="false" label="No wraparound (-w, --nowrap)" help="Use the actual input coordinates without any wraparound that would be needed by a circular genome. Without this option, the output sequence is the shorter of the two ways around the circle. Tick 'Specify sequence direction' to specify direction explicitly." />
  </inputs>

  <outputs>
    <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log" />
    <data name="exOutput" format="fasta" label="${tool.name} on ${on_string}: output" />
  </outputs>

  <tests>

  </tests>
  <help>
**What it does**

Read FASTA-format *sequence-file* and extract from it the subsequences specified by *coords*. By default, *coords* is the name of a file containing lines of the form *tag* *start* *stop* [*frame*] ...
Coordinates are inclusive counting from 1, e.g. *1 3* represents the 1st 3 characters of the sequence. For each line the corresponding region of *sequence-file* is extracted and output (after reverse-complementing if necessary).


**License and citation**

This Galaxy tool is Copyright © 2013 `CRS4 Srl.`_ and is released under the `MIT license`_.

.. _CRS4 Srl.: http://www.crs4.it/
.. _MIT license: http://opensource.org/licenses/MIT

If you use this tool in Galaxy, please cite |Cuccuru2013|_.

.. |Cuccuru2013| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2013) Orione, a web-based framework for NGS analysis in microbiology. *Submitted*
.. _Cuccuru2013: http://orione.crs4.it/

This tool uses `Glimmer`_, which is licensed separately. Please cite |Delcher2007|_.

.. _Glimmer: http://ccb.jhu.edu/software/glimmer/index.shtml
.. |Delcher2007| replace:: Delcher, A. L., Bratke, K. A., Powers, E. C., Salzberg, S. L. (2007) Identifying bacterial genes and endosymbiont DNA with Glimmer. *Bioinformatics* 23(6), 673-679
.. _Delcher2007: http://bioinformatics.oxfordjournals.org/content/23/6/673
  </help>
</tool>